Avian influenza virus detection and quantitation by real-time RT-PCR

Real-time RT-PCR (rRT-PCR) has been used for avian influenza virus (AIV) detection since the early 2000s for routine surveillance, outbreak assessment and for research. Some of the advantages of rRT-PCR are: high sensitivity, high specificity, rapid time-to-result, scalability, cost, and its inherently quantitative nature. Furthermore, rRT-PCR can be used with numerous sample types, is less expensive than virus isolation in chicken embryos, and since infectious virus is inactivated early during processing, biosafety and bio-security are also easier to maintain. However, the high genetic variability of AIV may decrease sensitivity and increases the chances of a false negative result. This chapter provides an overview of the USDA validated rRT-PCR procedure for the detection of type A influenza.